Transcription Start Sites (TSS)
Annotation of Transcription Start Sites in Drosophila
This walkthrough illustrates the GEP protocol for the comparative annotation of transcription start sites (TSS) in D. biarmipes. The walkthrough also includes a sample GEP TSS Report for the TSS annotation of onecut.
Module TSS1: Transcription Start Sites Introduction
This module describes how Celniker TSS annotations, DNase I hypersensitive sites, and the 9-state chromatin models can be used in the classification of promoter shape for the Antp gene. Exercise Answer Sheet Answer Key Exercise Answer Sheet Answer Key
Module TSS2: Using Sequence Alignment to Identify a TSS
This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis. Exercise Answer Sheet Answer Key Exercise Answer Sheet Answer Key
Module TSS3: CAGE, RAMPAGE, and RNA Pol II X-ChIP-Seq
This module uses the placement of the Initiator (Inr) motif, TSS annotations produced by the Celniker group at modENCODE, and experimental data such as CAGE, RAMPAGE, and RNA Polymerase II X-ChIP-Seq data to characterize the promoter for the Antp gene in D. melanogaster. Exercise Answer Sheet Answer Key Exercise Answer Sheet Answer Key
Module TSS4: Annotation of Broad Transcription Start Sites
This module illustrates the use of computational (e.g., blastn) and experimental (e.g., RAMPAGE, CAGE, RNA PolII ChIP-Seq) data to define the narrow and wide TSS search regions for genes with broad promoters. Exercise Answer Sheet Answer Key Exercise Answer Sheet Answer Key
Searching for Transcription Start Sites in Drosophila
This PowerPoint presentation describes the recommended annotation strategy for identifying transcription start sites in Drosophila. The presentation provides an overview of the promoter architecture in D. melanogaster and describes the types of evidence that can be used to support the transcription start sites annotations.
TSS Annotation Workflow
This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.
TSS Module Primer: Review of Transcription, Promoter Structure, and Chromatin Packaging
This primer includes some biological concepts that may be helpful to review prior to working with the four TSS Modules, including: a brief review of gene transcription, mRNA processing, promoter structure, and chromatin.
Faculty Resources
- All of the modules listed above are available with answer keys in a single package (automatic download) that uses members’ individual login credentials for the Project Management System.
- A new version of the TSS Quiz is currently being beta tested. See Assessment Tools for more details.
About
The Transcription Start Sites (TSS) modules were developed by Margaret Laakso, Jamie Siders, and Michael Foulk. We would like to thank additional members of the GEP who helped to review and revise these modules.
